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982 C.R

"Wait....Pinkie Pie?!" yelled Trixie, staring wide eyed at the Doctor. "Rarity said she'd been missing for years! What happened to her?"
The Doctor shook his head sadly. "Nothing good I'm afraid, Twilightwo's kingdom was a dark place...

35 T.R Castle of Lanterns

The three of them stood in shock. The pink pony lay on her side on the table, attached to medical wires and sensors Twilight didn't recognize. The lights around the room didn't leave a single shadow.
"I-Is she..." Twilight started.
"No, she's breathing, but it's shallow." The Doctor examined her, removing his goggles. "She doesn't even appear to be sick...." He took the sonic screwdriver from his pocket and scanned her. After a moment he frowned.
"What is it?"
"There's nothing wrong with her. Nothing at all, she's perfectly healthy, literally. Everything about her is just fine." The screwdriver fluctuated suddenly. "Wait, wait a minute." the Doctor squinted, scanning her again. The fluctuations were greater towards Pinkie's head. "Something is different. Something in her brain."
"Her brain?" asked Rarity. "What is it? What have they done to her!?" Rarity bristled as she spoke. "The poor dear's been missing for years. Has she been in this horrid place the whole time?"
Twilight stepped up to look at her friend, lying unconscious on the table. It was rare to see the bubbly pony sleeping. It was strange seeing her here, knowing that the darkness of this future had even affected her.
"What is it, Doctor?" Twilight asked soberly. "What's wrong with her?"
"I can't tell," he admitted. "But I think I know how we can find out." He turned to Twilight, she noticed he somehow looked even older than usual, he nodded to a small book lying on the ground. He'd apparently dropped it when he'd opened the door. "It's what I picked up, it appears to be a journal, my journal. We might find out what happened here if we read it."
Rarity's horn glowed, working better in the light, as she picked it off the ground. "This is your journal?"
"As much as I don't like it...I might have had a part in this." he looked at Pinkie soberly. "Knowing me, I would have written it down. It's a habit."
Twilight didn't know what to say. She took the journal from Rarity's grasp, and put a hoof on The Doctor's shoulder. "Whatever's in here, it's not your fault," she said.
The Doctor looked at her for a moment, then turned to Pinkie. "We need to get her out of here and back up to the castle." He walked over to one of the buzzing blue lights, poking it with a hoof. "This'll do nicely." He began scanning it with his screwdriver.
"What are you doing?" asked Rarity.
"The Vashta Nerada have been disturbed by the light, they're angry now; sick of holding back."
"Meaning?"
"Meaning that if we walked out of this lit area we'd be reduced to very clean bones in a matter of minutes."
Rarity blinked. "Oh."
"Yes, 'Oh'. But! Me, being as clever as I am, created these." He gestured to the long, buzzing bulbs around the room. "As far I can tell this is pure light. None of that diluted stuff you get from the sun, or a flashlight. These shadows are densely packed and they'd be able smother almost any light, but not this. If I can..." he scanned around the edges of the bulb, waving the screwdriver around widely. "There!" Two long rods of light clattered to the floor. He grabbed the nearest and tossed it to Twilight, who caught it in a glowing halo of magic. "Ms. Sparkle, you'll be leading the way. Make sure to keep that light as straight as possible, it is vitally important that it doesn't waver or shake in the least. Got it?"
Twilight nodded.
"Good girl." He turned and grabbed the other rod between his teeth. "I'll be bringing up the rear." he mumbled.
"Wait!" said Rarity, looking around the room. "What about me? Why don't I get a light?"
The Doctor mumbled something.
"What was that?"
The Doctor leaned his light against the table, then hefted Pinkie onto his back.
"I said, because you'll be carrying this."
"Oh," said Rarity. "Wait wha-"
She was cut short as the Doctor bucked Pinkie in her direction. Rarity grunted as she suddenly found herself carrying the weight.
"There we are! Onwards and upwards!" He ignored Rarity's glare as he turned to look at the two mares. "Now, remember, you musn't, not even for a second, step out of the light. It is vitally important. "Do you understand?"
They nodded..
"Good." He picked up the light rod. "Let's go."
Very carefully, Twilight got in front of Rarity, and began to march forwards. The Doctor settled in behind them, walking backwards and eliminating any lingering shadows. Twilight felt the pressure of the darkness around them, pushing against her as they once again made their way out of the workshop. Darlock bodies gleamed and twinkled in the blinding light, holding a strange dark beauty when illuminated, and twice as threatening when once again swallowed by the dark.
It was slow going, but eventually they found themselves back inside the first laboratory where the blue raggedy stood waiting. It tilted its head to the side as they approached, its button eyes glowing in the light.
"Melvin, take her, will you?" The Doctor pointed to the unconscious pony on Rarity was carrying
The cloth pony nodded and effortlessly hefted Pinkie onto its back, waiting for further orders.
Rarity sagged with relief, but it was short lived as the Doctor started off briskly back towards the stairs.
"I think we need to have a meeting of the minds." he said tersely, taking the stairs three at a time. Rarity and Twilight hurried behind him. Melvin, bringing up the rear, was simply happy to be useful.
Twilight quickly caught up, keeping pace at the Doctor's side. "We need to find out what your other self knows," she agreed.
"I'm more curious about what he doesn't know. According to Twilighttwo, I disappeared shortly before all this happened. That pony upstairs didn't recognize Fluttershy; she wasn't even sure he was the same pony from the crash all those years ago. He may be me, but something's happened to his mind, I can feel it."
"What....what could do that?" Twilight asked slowly.
The Doctor paused as he neared the top of the stairs, Twilight almost bumped into his rear as he stood there. He took a deep breath and let out a long sigh.
"Nothing good." Without another word, he continued upwards.
The journey back to the small room in which the Doctor's double lay sleeping took less time than the journey down had been. Twilight noticed that whatever dark force was laying in wait in the air seem to part as the Doctor walked forwards. From her position behind him she could almost feel it, something coming off of him. She had a feeling that the next thing that came too close, would burn.
They came back up into the small, cluttered room that made up Tick-Tock's living quarters. Though the room was nowhere near as bright as the rest of the castle, they had to squint until their eyes grew accustomed to being out of total darkness. As Twilight climbed the final step onto the level floor, she felt as though the dark clung to her a bit, like water after jumping into a cold lake. She shook herself involuntarily and Rarity did the same.
The Doctor never paused. Fluttershy stood in the corner of the room fretting over Tick-Tock as he lay unconscious, the Doctor firmly pushed her aside staring at his double. She began to say something, but whatever it was died in her throat when the raggedy hauled itself from the stairs. First her eyes flashed in fear, immediately backing to the far wall, but as they fell upon the pink pony lying prone on its back, they flashed with something else, something old.
"Pinkie," the word came out as barely a whisper. In a flash, fear totally gone, she was lifting her from the Raggedy's back and laying her on the floor, checking every inch of the pale earth pony. "Oh my gosh...Pinkie..."
Twilight stepped up to her, placing a hoof on her side. "We found her...down below, in his workshop." She nodded to the unconscious scientist the Doctor was examining.
Fluttershy froze. "She was...."
Rarity came up and nodded. "Lying on a table hooked up to some machines. There's no telling how long the poor dear's been down there..."
Fluttershy stared at her friend for a moment, then back to Tick-Tock. "But...he...he wouldn't..." She looked at her two friends desperately. "He....I...I can't believe he had any part in this...he's sweet...and kind....and...and..."
Twilight put a hoof around the yellow pegusi's shoulder. "It's alright...we'll get to the bottom of this..don't worry."
The Doctor let out a snarl of frustration from the corner of the room, his forehead pressed to Tick-Tocks.
Rarity gasped with fright. "Doctor stop! Don't touch him, you'll cause another Paradox!"
"We're already too far gone for that." He said with a sigh of resignation. "His head...someone's been messing with it, periodically for a number of years if I had to guess...He...I...Don't remember a single solitary thing about anything that happened before all this."
Twilight walked over and looked down at the other Doctor breathing a bit fitfully in his bed. "Can you see what happened during that time?"
The Doctor shook his head. "Nothing, there's some heavy duty blocks set up...probably by Twilighttwo."
Twilight blinked. "Me?....I'd neve-"
"Stop there," he said quickly. "None of this is your fault. Not even a little..." He said something under his breath, but before she could ask he whipped something out of his suit pocket. "I may not be able to see what happened, but we might be able to read it."
Rarity trotted over, studying the small slightly beat up book the Doctor had produced. "What's that?"
"Tick-Tock's diary!" Fluttershy exclaimed, looked up from the sleeping Pinkie Pie. "I...where did you find that?"
"Kept it on him at all times." The Doctor nodded, examining it. "Probably so nopony would stumble upon it. Curious nurses included."
Fluttershy turned a brief shade of red, and quickly went back to examining Pinkie.
"By the looks of it it's pretty old. Should be able to tell us a thing or two about what happened while we were gone from a unique perspective....my perspective."
Rarity gulped. "Well...what are we waiting for?...As you say...Onwards and upwards..."
"Indeed....Twilight would you do the honors? As much as I'd like to I'm not greatly used to hooves just yet and turning pages is beyond me."
Twilight eyed the tome for a few moments, before taking a deep breath. "Okay." She cast a glance at the sleeping Pinkie Pie... "Let's find out just what's going on here."
She began to read.

Good Evening Dear Diary,

My name is apparently Tick-Tock, I have no prior memories before this date, so I have decided to start chronicling my thoughts to prevent any further loss.
I currently find myself in a small town by the name of Ponyville. I am under the care of a mare by the name of Twilight Sparkle, by whom I was found a few days ago in the Everfree forest. She nursed me back to health and I have only recently awoken. I am very thankful for her hospitality, though at times she seems quite brash. There is something there, in those eyes of hers that I find quite unsettling. But it is not for me to say, she has provided me with room and board until my memory can be regained, I have no place for criticism next to such a generous offer.
She says I am a scientist, and I believe this to be true, I have a profound interest in the way things work. Even now I find myself wondering about the workings of this town, though I have no personal knowledge of my past my mind is filled with calculations and ideas that I itch to bring forth into the world. Hopefully when I am well I will be able to.

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"Skip ahead a few entries," said The Doctor, whatever happened it had to have been in recent years."
Twilight flipped through a few pages.

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Once again I must confide in you dear diary,

I have been under Twilight's care for several months now, but as of late I have hardly seen her. She has locked herself away in the basement of this great library, and is hard at work on something.  She has asked my help several times, but has never let me see the device she is attempting to build. I have asked her companion, a small dragon by the name of Spike, but he knows little more than I. We find ourselves in each other's company more often than not. He is a pleasant if at times childish fellow. From what I gather he and Twilight were quite close at some point. I must wonder if perhaps there was some kind of fallout, as Twilight hardly says a word to either of us in the rare times when she comes out of the basement. Despite this he still seems loyal to the last. The eyes, as I have noted in many entries, have gotten even darker than my last. I worry there is something wrong with the poor girl, but she will not let me examine her. I am beginning to fear for her, though I am as of yet not sure if my worries are warranted.

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Twilight flipped through the next few entries.
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Diary I must cite an odd happening this evening,

There was a knock at the door as I was reading a tome of Equestria history. I have never answered the door, as Twilight has requested I not do so. While I find this an odd request she has been kind to me in her own, distant way, and it would not be right of me if I did not try to adhere to any rules put forth.
I tried my best to ignore this intrusion and continue my studies, but oh diary this visitor was persistent, for hours they hammered at the door until I could not take the noise any longer. I had been living here for nearly a year now, had I not? I thought myself entitled to a little peace, and what harm could it do?
So, emboldened by my annoyance, I opened the door to find a pink pony standing there. I had spied her from afar several times, normally from a window, or among those who visited Twilight every now and again. I opened my mouth to try and tell her that Twilight was busy, but suddenly found myself enfolded in one of the most constricting hugs I have ever endured!
The strange visitor began talking so fast I could hardly comprehend what she was saying. You've never heard such madness! Stories of stone angles, alternate dimensions and doctors, I do fear she is quite mad.
But this is not the strangest thing, dear diary. The strangest is...I find her madness contagious! For no reason I can describe I found myself incomparably happy to see her. As though we were old friends seeing each other anew. Does it have something to do with my lost memories? Even her ramblings seemed oddly familiar. Of course they are utter nonsense, but nonetheless I feel a connection, such a profound feeling that they are somehow important.
But alas, dear diary, before I was able to question her further Twilight came storming out of the darkness of her basement. You've never heard such screaming!
She was furious that I had dared to answer the door, or that this pink visitor should try to talk to me. As she was yelled at the poor girl she looked as though she'd been psychically struck.
Twilight slammed the door in a rage, and shooed me back up into my room, where I have remained for the last day or so. The door has been locked, I am afraid I have angered her quite thoroughly this time. It appears the door rule is to be obeyed at all costs.

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Dear Diary,

It has been mere hours since my last entry, I find that I cannot sleep as nightmares plague my rest. I see such strange things! Stone Pegasus and animate dolls, aliens of all shapes and sizes! Mechanical dogs and bipedal creatures I cannot describe. But I feel as though I know them, that I know this world of dreams. Oh, curse my lack of memory! If only I could fathom there meaning, but alas I cannot.
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The next few pages were filled with sketches, Twilight flipped through them slowly. Some she recognized, and others she did not. One of them appeared to be a Darlock, only without the horse shaped upper portion. It had been circled several times in red.
"Keep reading!" said Rarity.
Twilight quickly flipped through the drawings, and continued. The next few entries recalled fantastic accounts of dreams, and their significance, but nothing of particular interest. She continued through the journal until she found something.

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Dear Diary,

I must apologize for my lack of entries the past few days. I have been busy. Twilight has been asking me more questions than usual, and generally requiring more of me on a day to day basis. I must wonder if it is because she really requires my assistance. Or is simply trying to keep me busy, if Spike is  correct, then I have been talking in my sleep. This apparently has her worried, is she trying to fill my mind by supplying me with other tasks so my dreams will turn to other subjects?
I cannot help but wonder.

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The page following the entry were filled with more Sketches, this time of a small wooden box with
glass in the front.
"The HORN," said the Doctor. "Keep reading, we're coming close to the big event that brought on your rule."

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Diary, something wonderful has happened,

I cannot remember my last entry, for I have been so very busy. You see, dear diary, Twilight has given me access to what she has been working on for all this time.
I have made several sketches, I am not sure of all of it's workings, for sadly I am not a unicorn. But diary that's the thing! Soon I will not have to be! The mechanics are complex, which is why she required my help, but I believe that with this device magic will no longer be reserved for those special few born with the talent! We have worked through the night and she plans to unleash this gift upon the world in mere hours. The excitement is palpable.

------------------

Dear Diary,

I apologize for being haphazard with my updates. It's marvelous, there are several of the devices currently in operation around ponyville. While I myself have not had the honor, it is a wonder to see them in action. HORNs they are called, and such fantastic things they are. Magic for earthponies? A mere dream for many a  young foal, now realized! I can hardly believe it. It seems my fears of Twilight were unfounded. She is an inventor after my own heart, and she has changed the world for the better. She has taken the invention to Cantolot, where I have heard there is trouble. Hopefully it shall be able to help. The princesses, from what I've studied, have been ill for some time. Twilight has taken to helping, making decisions by way of letter. Who knows, with this invention perhaps they can be cured? With this device anything is possible. It will be a golden age for Equestria! And I had a hand in it, though I can remember nothing of my past, I have bright hopes for the future.

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Dear Diary,

I write this in fear, Twilight has returned, and she has changed. Her eyes have taken on the darkest color I have seen on any living creature. This evening I heard her talking to herself in the dark of the basement. I dared not intrude on whatever dark things she's working on. Spike seems just as worried, he has grown, almost too big for the library at this point. I am worried for him as well as Twilight, he is tired as of late. It seems he has some part in the production of the HORNs, but he will not reveal to me what it is. For the last several days he has been more private than usual. When pressed he simply replies 'It's what's best for Twilight.' It is unsettling. I do not know what will happen next, but I feel in my heart that it shall not be good.
---------------

Twilight stopped reading suddenly. The Doctor a hoof on her shoulder.
"I...I think I can deal with the hooves...Would you like me to read the rest?" he asked softly.
Twilight nodded.
The Doctor grabbed the book from it's place in the air, and placed it open on the table
next to the unconscious Pinkie Pie.
"Just remember. None of this is you, time is in flux, never more so than now."
He continued to read.

-------------
Dear Diary,

My worst fears have been realized. Twilight departed for the lantern castle in the Everfree Forest several hours ago, and even from here I can feel the shaking. Something dreadful is happening as I write this account. The entire town has been up all night looking, looking towards the flashes above the trees. It is now nine in the morning, and the sun has not yet risen, it lies on the cusp of the horizon, daring to go no farther. I know I cannot be sure Twilight's hoof is in this, but it is as if I can feel that she is. That something is now wrong with the world, wrong with time itself. I feel compelled to go forth, to do something to stop it. But do not know how I can help. So I remain here, a coward. We can only wait until the noise ends, and hope for the best.

-----------

Things are grave indeed,

She's queen now. Twilight has installed herself as the monarch of Equestria, she's changed, I know not what happened to the princesses, but Twilight now shares their form. She is an alicorn, normally a creature of dreams, turned to a nightmare.
The sun still has not risen, as I stand here, several days from my last entry. It is twilight, it seems, for eternity.
I am packing what little I have. I received a letter stating I have been summoned to Cantorlot, where I am to live, Spike has already gone ahead. Who are we to disobey the queen?
We are no one.

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I have arrived Dear Diary,

The opulence of Cantorlot is lost on me. I have never been far outside of the Library in Ponyville, Twilight never allowed me the pleasure, but in this darkness is there any point?
Alas, I must apologize for being so morose, dear diary, but things are in quite a state. Twilight rules with an iron hoof. It has been mere days since her take over, and already she has launched armies against the Griffin Kingdoms and the mines of the Dimond Dogs. I fear she has been corrupted beyond any help.
Sadly, my stay is not to be long here. Already I have been ordered onto a train that leaves in a few hours. To the Lantern Castle in the Everfree, what she plans for me there I have no idea.
-------------

The Doctor flipped the middle of the diary, many of it's pages singed beyond comprehension, he frowned, and continued to nose through until he got to something legible.

------------

Curses, another failure, and it seems I have burned a large chunk of my records in the explosion. Years of writings, gone. Never to be replaced! Well, I have never been one to dwell on that which cannot be changed. According to what pages remain my last surviving entry is from before I arrived. To reiterate any lost knowledge, I have been here for the past...how long has it been? It is hard to keep track in this dark laboratory.The dark that makes you feel you're not alone.
Day and night are meaningless in anycase. To continue, I have continued work on Twilight's newest tool of war. They have been shipping out for months, and I am beginning to scare myself, but I have no choice but to continue. If I do not she has not only threatened to hurt me, but my only companion. A nurse by the name of Fluttershy, she is charged with the care of the Princesses, who have been in an awful state since Twilight came to power. She brings me food every now and again, and is a kind soul. I could not bear to see her hurt. But I must wonder dear diary, if I have been making the right choice all these years? I feel such loathing for my creation, the Darlocks. I look upon them now, their lone eyes staring back at me, a small bit of life in each.
I have at least done some good in that respect. I do not know how, but I knew what to do the second I began work on them so long ago, and what Twilight wanted me to do. To use ponies, to power these cruel machines....I could not bring myself to do so. So I have delved into deep science. Things which are new, and scary to me. I have grown them, from mere samples of myself. Bits of hair and skin. They are my children....which makes me loathe them even more. Alas, the alternative is unfeasible.
Still I am bothered, it seems my cells are not normal. they grow many times faster than that of any other creature I have encountered when cultivated, and are devilishly hard to kill. I have begun to wonder.
What am I?
---------------

Dear Diary

I have received new plans, plans for a machine under the capitol. It's awful.
I know why I don't feel alone in the dark. I know what she's planning. Yet I have no choice.
Once again I find myself a coward. I dare not write further on the subject.

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Dear Diary,

I have begun to understand the darkness better. Through study I have found that it is not one mass, but several smaller, almost microbial life forms feeding in the air. They make up the blackness around me. That is why my laboratory must stay in the dark. They are part of the Darlocks, but not only that, they are my guards, and her insurance, they could devour me in seconds. Or Fluttershy for that matter, should they get the inclination. I now know why the princesses were raving, why they constructed the castle above me, filled with lights to banish the shadows. I know why they are afraid of the dark. If only they knew what lay below them, it would scare them to death.
Yet I am unharmed. I must wonder how she controls them. If I can figure that out, I will no longer be in danger, perhaps then we can escape.
But where would we go? She cannot leave the princesses unattended and they are hardly in any shape to travel. Twilight would find us in a matter of days if not hours. It seems a hopeless task.

---------------

Dear Diary,

Suddenly I feel as though Fluttershy and I are not alone in this castle. I have grown used to the Darkness's intrusion, but it feels as though there is something new. I am cautious, it may be some new agent of Twilight's power, sent to keep an eye on me. I am wary.

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Dear Diary,

Let me start from the beginning for the first time in many years I feel hopeful. My fears of a new threat have proven wrong, in fact we have a new ally. One that is desperately needed.
It happened yesterday. I had come out of the lab in order to have lunch, Fluttershy had scraped together something extra from the Princess's meager stores in order to spice up the usual hay and oats. She does what she can to make our lives a touch brighter. It made me feel a touch poorly for taking lunch alone. My years of solitude seem to have left their mark.
In anycase, I was eating as usual when suddenly right behind me I heard laughter....Such a curious thing, not only for it's abruptness, but because it had been so long since I'd heard any. I was badly frightened by this, spilling my lunch all over the floor.
But when I turned to find the source of the sound I saw her.
The pink pony from all those years ago. The one at the door who spoke of nonsense, she was standing right there, as smile on her face bigger than any I'd ever seen.
My fear was replaced by sheer amazement. How had she found me? Or gotten here? She wore the official clothes of the royal planner. I thought for a moment that perhaps she was here to deliver a message, or some news from the capital. Before I was able to voice any of my many questions I found myself once again in a hug which forced all the air from my lungs, apparently her customary greeting. She, Pinkie Pie, called me 'Doctor' and rattled on so fast I couldn't understand a word after that.
Once she calmed down she informed me that she has run away from Twilight's castle in Cantorlot, where she has been employed for the last couple years. Apparently because Twilight has 'Become a meany.' which is the single biggest understatement I shall ever write.
She apparently found me by way of 'Pinkie Sense' whatever the term may mean. She said she had the feeling that something big was about to fall, and pointed to her ever moving tail as a reference. I still understand little of this, but I am glad to have another friendly face. Her happiness is ever contagious, I find myself smiling as she dances about the room, talking faster than I can comprehend.
She says we must keep her presence a secret from Fluttershy. Ponies will come looking for her, and Fluttershy is far too sweet to lie, or at least lie well. So her ignorance is best for the time being. She offered to hide in my lab which I was vehemently against, knowing what darkness lies there.
Still she marched on, unafraid, to the edge of the stairs, where the light ended. She knew what was down there, and simply reasoned with it.
I don't know how, or why this worked, but she said that there was only supposed to be one pony down there, so therefor if she was going down there with me willingly knowing what might happen, then she must not be a pony.
Then she stepped downwards. Into the dark.
And was fine.
I've often wondered, since discovering my cells seem abnormal, what I am. Now I find myself wondering....What is she?

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Dear Diary,

It seems Pinkie was right, Twilight has begun a massive search for her. A pair of those awful living dolls she employs searched the castle today. Fluttershy says she's never seen the princesses so scared. Still, as Pinkie predicted, they did not look inside the lab, and left having found no trace of her. It seems she is safe for the time being.

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Dear Diary

I have told Pinkie of Twilight's plans for what lies beneath the castle, and of my hand in it. She was just as dismayed as I to learn of this. We have begun to plan against it. We have nothing yet, but we must stop her terrible ambitions, lest everything we know, and in fact what we do not, be threatened.
While we worked she continued to tell her stories, the same ones from when we first met. Apparently this 'Doctor', whom she believes to be me, is some kind of hero. I am far from this. I have told her of this mistake, I am but a scientist, but still she persists. Saying I knew her, and Twilight before waking up with nothing all those years ago, saved Equestria. I wish this were true, it would explain the ever present gap in my memory. But it is simply absurd.
All they are is stories...

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Dear Diary

It has happened. She is here, to check on my progress, queen Twilight has come here, and she is even  less the mare I once knew than ever. I have shown her the Darlocks, almost ready for her evil plans, while Pinkie hides among the Princesses. Fluttershy is still nonethewiser. This is perhaps for the best, Pinkie Pie was correct, the poor sweet hearted mare was almost in tears from the simplest of questions on the princesses' status. Feeling guilty for giving me what food she could. I cannot imagine burdening her with such a secret.
But, hiding Pinkie Pie shall not be easy, Twilight appears to be staying for the next few days to monitor my work. I fear that she knows more than she is letting on.

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Dear Diary
I am not sure whether I should be happy, or sick to my stomach. Twilight is very pleased with my efforts towards creating her war machines. She plans to leave tomorrow night to begin preparations. I dearly fear what may happen, but at least we shall be rid of her, and we'll have the time we need.
Time.
What a funny concept these days. After all these years, I, nor Fluttershy nor Pinkie has aged a single day....I believe the HORNs have something to do with it...but...I've never had a Horn. So I must wonder...what is my excuse?  My theory must be flawed. In anycase, Pinkie and I have come up with a plan to stop her, a device which, when planted into the machine under the capital will disable it, and perhaps allow me time to make sure it never sees its terrible work done...for you see Twilight has ruined one world...I shall not let her ruin another.

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All that planning....to waste...She found us....She came...into the laboratory the night she was set to leave, totally unannounced....Pinkie Pie was hidden among the monstrosities, but I think we both knew something was off. She seemed a bit too happy....Twilight circled the lab like a shark, taking glee in my fear. She said she'd never seen the Darlock's newest weapon in action, and that it would be nice to test it. She was cruel in her teasing...she offered to go and grab Fluttershy for a test run, and that was all Pinkie could take. She leapt out of the darkness with and offered herself to Twilight in the poor nurse's place. I leapt to protect her, but found myself wrapped in the bonds of Twilight's ethereal tail, forced to watch as she was punished for betraying the queen.
The funny thing is...Pinkie seemed happy to see Twilight, for all she had done...the poor girl smiled and laughed, even joking as the queen activated one of the monsters. And for a moment... just for a moment, Twilight's eyes lightened, and she looked sad. Genuinely and properly sad. But, like anything in this horrid lab, it was quickly extinguished as the newly awakened darlock fired, striking Pinkie squarely in the chest. Her laughter stopped, and her color faded.
You see, the darlocks are not a forceful weapon...no...the darkness that permeates my workspace is part of them....and that darkness...that horrible...oppressive darkness can do more than devour...it can change. Smother the synapses and darken the mind as well as the air. Taking joy and happiness and leaving mindless drones...this is what she plans for Equestria....and worlds beyond...darkness, inside and out...eternal twilight of the body and mind. A ever feeding, ever growing stain upon the universe.
And I let it happen.
I sat there as Pinkie's happiness was drained away in an instant.
Or at least as the darkness tried to.
You see, I think that some people are just happy...naturally...properly happy. They're few and far inbetween...but if anyone is...it's Pinkie. There is a light inside her so bright that it could outshine the hidden sun. And no amount of science or magic, could ever truly change that.
She fought, dear diary. Her mane and tail went straight as silk, but still, she smiled a bit at Twilight, and said she'd see her soon, in happier times. She danced about the lab like a filly, occasionally grimacing or struggling, but doing so nonetheless. Twilight was put momentarily enraged....but for some reason...she did not strike out against the pink pony...I think that light inside stopped her...that bit of good still fighting among the darkness as Pinkie did then. She simply left. Leaving Pinkie barely standing among the darlocks. She released me and vanished into the night to put her horrible plans into action.
I had little time to act....I gave Pinkie a sedative of my own creation, I have applied a dose every few hours. It slows the process going on in her head....but I wonder to what end? Hers is perhaps the fate that awaits us all....still I must...I must have hope. There is a light in her, and I think that perhaps that light, a light that is in every being that has ever known joy, may be the only thing that can stop the darkness. If I am wrong, then all is lost. I dearly hope some poor soul should figure this out, as I am too afraid to act further. If I do, I fear what may happen to Fluttershy and the princesses. I continue my work in my prison...alone.

---------------

The journal entries ended, the Doctor closed the book with a sharp thud. He stared hard at the small journal for several moments, then down the stairwell. Twilight sat on her haunches, exhausted by all the information she'd taken in.
Rarity made a quite sound. "They're...made from you....and Pinkie....Twilight she..."
The Doctor simply nodded his expression never changing.
Twilight took a deep breath. She looked back at Tick-Tock who's breathing had grown more fitful as they'd read.
"I....did that...to you?"
The Doctor's head whipped around to look at her, she didn't flinch. He stared at her for several seconds, his deep blue eyes burning with something deep and old.
He was the first one to break away. "No..." The Doctor looked at the ground. "I was the one that did this to you..."
Twilight paused. "Doctor...what do you mean?...Did what?"
The timelord sighed. "You've known things...since the toyshop haven't you? I've pointed it out before now, kept saying I'd explain later...But...perhaps I was hoping it wasn't true."
Rarity stared at the Doctor worriedly. "What...wasn't true?"
"Back in our present, to stop the reaper I let you look into my head...but I underestimated you...and gave a lot more than I intended...You may have already guessed that much."
Twilight nodded. "I've...been thinking about it since I knew how to fix the TARDIS...back before we came here."
"Well, that alone was not enough to make you do all of this. Back then, way back, when we were looking for her." He pointed to Fluttershy, who made a soft surprised noise. "She said her bunnies had gone missing, and I thought that the reason must've been some sort of predator, something that was already in the habitats."
"Yes..." Twilight prompted.
"I didn't have the time to think about it, but what's in every rabbit hole? Every din and every burrow? A shadow." He gestured towards the stairwell, the light stopping after the first step to be swallowed by the dark. "And in the dark, sometimes things go missing...the Vashta Nerada. So, in that chain of events, you, Twilight Sparkle, got a bit of timelord in your head, and I, put it there."
"So lets say this timeline ran a bit differently. Let's say that you and I solve this problem, or its a different one, or we somehow make it back home. Then we go investigate the 'Strange creatures in Fluttershy's little garden.'" The Doctor laughed almost ruefully. "And what do they find when Twilight Sparkle bumbles into the dark? A meal? Oh, oh no, they find something greater than that. You see, me? All that knowledge is safely locked up in my head, they could eat me if they like, it'd take'em a while with the regenerations and all, but they could, and nothing'd happen. But you...oh your mind is wide open. And as they set in...they find a spark of knowledge so great it inspires them...tells them they can do more than eat, more than just mindlessly feed...that they can rule. And oh here's the perfect little vehicle to do it in. Just turn down the light in that mind a little, just a touch here and there, tiny things at first. Then they start to turn up the dark. Slowly and steadily altering you, microscopic spores of darkness in your head." He turned to her, his face sad and lonely. "With all the darkness around us now, they might have started again already....a chain of events going round and round, I take you back, you run into them, they change you...you become ruler of Equestria and set out to spread darkness wherever you can. All because I was too stupid to notice." The Doctor took Twilight's head between his hooves, and planted a small kiss on her forehead. "I'm sorry Twilight Sparkle. Very, very sorry. But this is not your fault. It's mine."
Silence filled the room, heavy and thick for several minutes. The only sounds the soft breaths of the two sleeping ponies on either side of them, each going through their own nightmares.
"How do we stop it." Twilight said finally.
The Doctor didn't say anything.
Twilight repeated herself. "How.Do we. Stop it."
Rarity gave the Doctor a hopeful look, but he remained silent.
"Doctor?" Twilight said.
He managed, to look up, only for a hoof to meet the side of his jaw. He spun a bit before falling to the ground.
"Hey!" He yelled.
"You will not give up on me." Twilight stood over him fuming. "You fall out of the sky into my house, get me kidnapped by evil statues, destroyed several reputable businesses around Ponyville, implant the knowledge of an ancient race into my brain, get me flung into a horrible future where half my friends are under my tyrannical rule, my mentor is half crazed, the sun never rises and there are living dolls roaming the streets, and you think I'm just going to let you sit there like an idiot?"
The Doctor looked up at her, totally stunned.
"If you do then you've got another thing coming. Now get off your flank, get that sonic screwdriver of yours, out of your coat pocket, and help me fix this. Now. I'm tired of being scared of everything, I'm tired of worrying that I'm going to be some horrible pony fifty years down the line. And I'm really sick of my friends being treated this way by someone who will never be me. I don't care what you did, what you've done, or what you're going to do. What you're doing now is fixing this. Are. We. Clear?"
Both the Doctor and Rarity stared at Twilight mouths agape.
"Well," The Doctor was the first to speak. "When you put it that way." He hopped up and headed towards Tick-Tock. "Let's get started. Melvin, pick up Pinkie Pie." The Doctor hefted Tick-Tock onto his back, then flung the unconscious pony in Melvin's general direction, despite Fluttershy's weak protests. "This too, who knows, I might be useful eventually." He headed towards the door out into the castle proper.
"That's more like it." Twilight joined him at his side, a still stunned Rarity bringing up the rear. "Where are we going?"
"We need to have a word with your mentor, and then we need to find transportation. Quickly."
"So we can get back to canterlot and find the TARDIS?"
The Doctor nodded. "That and because if my ears don't fail me, there's a train coming."
Rarity blinked. "There's only one other train that comes this way..."
"Twilighttwo's personal locomotive?" The Doctor guessed.
Rarity looked worriedly towards the nearest window. "Um...yes."
"Figured that, with a full complement of fully functional Darlocks no doubt."
Twilight stared at the two of them for a second, before quickening her pace. "Yeah...Let's hurry."

982 C.R

"Then what happened! Then what happened!" Trixie yelled, jumping up and down as the Doctor spun his tale.
He gave her a little smile and said.
"Then came the hard part."

To be continued.

Description
982 C.R

"Wait....Pinkie Pie?!" yelled Trixie, staring wide eyed at the Doctor. "Rarity said she'd been missing for years! What happened to her?"
The Doctor shook his head sadly. "Nothing good I'm afraid, Twilightwo's kingdom was a dark place...

35 T.R Castle of Lanterns

The three of them stood in shock. The pink pony lay on her side on the table, attached to medical wires and sensors Twilight didn't recognize. The lights around the room didn't leave a single shadow.
"I-Is she..." Twilight started.
"No, she's breathing, but it's shallow." The Doctor examined her, removing his goggles. "She doesn't even appear to be sick...." He took the sonic screwdriver from his pocket and scanned her. After a moment he frowned.
"What is it?"
"There's nothing wrong with her. Nothing at all, she's perfectly healthy, literally. Everything about her is just fine." The screwdriver fluctuated suddenly. "Wait, wait a minute." the Doctor squinted, scanning her again. The fluctuations were greater towards Pinkie's head. "Something is different. Something in her brain."
"Her brain?" asked Rarity. "What is it? What have they done to her!?" Rarity bristled as she spoke. "The poor dear's been missing for years. Has she been in this horrid place the whole time?"
Twilight stepped up to look at her friend, lying unconscious on the table. It was rare to see the bubbly pony sleeping. It was strange seeing her here, knowing that the darkness of this future had even affected her.
"What is it, Doctor?" Twilight asked soberly. "What's wrong with her?"
"I can't tell," he admitted. "But I think I know how we can find out." He turned to Twilight, she noticed he somehow looked even older than usual, he nodded to a small book lying on the ground. He'd apparently dropped it when he'd opened the door. "It's what I picked up, it appears to be a journal, my journal. We might find out what happened here if we read it."
Rarity's horn glowed, working better in the light, as she picked it off the ground. "This is your journal?"
"As much as I don't like it...I might have had a part in this." he looked at Pinkie soberly. "Knowing me, I would have written it down. It's a habit."
Twilight didn't know what to say. She took the journal from Rarity's grasp, and put a hoof on The Doctor's shoulder. "Whatever's in here, it's not your fault," she said.
The Doctor looked at her for a moment, then turned to Pinkie. "We need to get her out of here and back up to the castle." He walked over to one of the buzzing blue lights, poking it with a hoof. "This'll do nicely." He began scanning it with his screwdriver.
"What are you doing?" asked Rarity.
"The Vashta Nerada have been disturbed by the light, they're angry now; sick of holding back."
"Meaning?"
"Meaning that if we walked out of this lit area we'd be reduced to very clean bones in a matter of minutes."
Rarity blinked. "Oh."
"Yes, 'Oh'. But! Me, being as clever as I am, created these." He gestured to the long, buzzing bulbs around the room. "As far I can tell this is pure light. None of that diluted stuff you get from the sun, or a flashlight. These shadows are densely packed and they'd be able smother almost any light, but not this. If I can..." he scanned around the edges of the bulb, waving the screwdriver around widely. "There!" Two long rods of light clattered to the floor. He grabbed the nearest and tossed it to Twilight, who caught it in a glowing halo of magic. "Ms. Sparkle, you'll be leading the way. Make sure to keep that light as straight as possible, it is vitally important that it doesn't waver or shake in the least. Got it?"
Twilight nodded.
"Good girl." He turned and grabbed the other rod between his teeth. "I'll be bringing up the rear." he mumbled.
"Wait!" said Rarity, looking around the room. "What about me? Why don't I get a light?"
The Doctor mumbled something.
"What was that?"
The Doctor leaned his light against the table, then hefted Pinkie onto his back.
"I said, because you'll be carrying this."
"Oh," said Rarity. "Wait wha-"
She was cut short as the Doctor bucked Pinkie in her direction. Rarity grunted as she suddenly found herself carrying the weight.
"There we are! Onwards and upwards!" He ignored Rarity's glare as he turned to look at the two mares. "Now, remember, you musn't, not even for a second, step out of the light. It is vitally important. "Do you understand?"
They nodded..
"Good." He picked up the light rod. "Let's go."
Very carefully, Twilight got in front of Rarity, and began to march forwards. The Doctor settled in behind them, walking backwards and eliminating any lingering shadows. Twilight felt the pressure of the darkness around them, pushing against her as they once again made their way out of the workshop. Darlock bodies gleamed and twinkled in the blinding light, holding a strange dark beauty when illuminated, and twice as threatening when once again swallowed by the dark.
It was slow going, but eventually they found themselves back inside the first laboratory where the blue raggedy stood waiting. It tilted its head to the side as they approached, its button eyes glowing in the light.
"Melvin, take her, will you?" The Doctor pointed to the unconscious pony on Rarity was carrying
The cloth pony nodded and effortlessly hefted Pinkie onto its back, waiting for further orders.
Rarity sagged with relief, but it was short lived as the Doctor started off briskly back towards the stairs.
"I think we need to have a meeting of the minds." he said tersely, taking the stairs three at a time. Rarity and Twilight hurried behind him. Melvin, bringing up the rear, was simply happy to be useful.
Twilight quickly caught up, keeping pace at the Doctor's side. "We need to find out what your other self knows," she agreed.
"I'm more curious about what he doesn't know. According to Twilighttwo, I disappeared shortly before all this happened. That pony upstairs didn't recognize Fluttershy; she wasn't even sure he was the same pony from the crash all those years ago. He may be me, but something's happened to his mind, I can feel it."
"What....what could do that?" Twilight asked slowly.
The Doctor paused as he neared the top of the stairs, Twilight almost bumped into his rear as he stood there. He took a deep breath and let out a long sigh.
"Nothing good." Without another word, he continued upwards.
The journey back to the small room in which the Doctor's double lay sleeping took less time than the journey down had been. Twilight noticed that whatever dark force was laying in wait in the air seem to part as the Doctor walked forwards. From her position behind him she could almost feel it, something coming off of him. She had a feeling that the next thing that came too close, would burn.
They came back up into the small, cluttered room that made up Tick-Tock's living quarters. Though the room was nowhere near as bright as the rest of the castle, they had to squint until their eyes grew accustomed to being out of total darkness. As Twilight climbed the final step onto the level floor, she felt as though the dark clung to her a bit, like water after jumping into a cold lake. She shook herself involuntarily and Rarity did the same.
The Doctor never paused. Fluttershy stood in the corner of the room fretting over Tick-Tock as he lay unconscious, the Doctor firmly pushed her aside staring at his double. She began to say something, but whatever it was died in her throat when the raggedy hauled itself from the stairs. First her eyes flashed in fear, immediately backing to the far wall, but as they fell upon the pink pony lying prone on its back, they flashed with something else, something old.
"Pinkie," the word came out as barely a whisper. In a flash, fear totally gone, she was lifting her from the Raggedy's back and laying her on the floor, checking every inch of the pale earth pony. "Oh my gosh...Pinkie..."
Twilight stepped up to her, placing a hoof on her side. "We found her...down below, in his workshop." She nodded to the unconscious scientist the Doctor was examining.
Fluttershy froze. "She was...."
Rarity came up and nodded. "Lying on a table hooked up to some machines. There's no telling how long the poor dear's been down there..."
Fluttershy stared at her friend for a moment, then back to Tick-Tock. "But...he...he wouldn't..." She looked at her two friends desperately. "He....I...I can't believe he had any part in this...he's sweet...and kind....and...and..."
Twilight put a hoof around the yellow pegusi's shoulder. "It's alright...we'll get to the bottom of this..don't worry."
The Doctor let out a snarl of frustration from the corner of the room, his forehead pressed to Tick-Tocks.
Rarity gasped with fright. "Doctor stop! Don't touch him, you'll cause another Paradox!"
"We're already too far gone for that." He said with a sigh of resignation. "His head...someone's been messing with it, periodically for a number of years if I had to guess...He...I...Don't remember a single solitary thing about anything that happened before all this."
Twilight walked over and looked down at the other Doctor breathing a bit fitfully in his bed. "Can you see what happened during that time?"
The Doctor shook his head. "Nothing, there's some heavy duty blocks set up...probably by Twilighttwo."
Twilight blinked. "Me?....I'd neve-"
"Stop there," he said quickly. "None of this is your fault. Not even a little..." He said something under his breath, but before she could ask he whipped something out of his suit pocket. "I may not be able to see what happened, but we might be able to read it."
Rarity trotted over, studying the small slightly beat up book the Doctor had produced. "What's that?"
"Tick-Tock's diary!" Fluttershy exclaimed, looked up from the sleeping Pinkie Pie. "I...where did you find that?"
"Kept it on him at all times." The Doctor nodded, examining it. "Probably so nopony would stumble upon it. Curious nurses included."
Fluttershy turned a brief shade of red, and quickly went back to examining Pinkie.
"By the looks of it it's pretty old. Should be able to tell us a thing or two about what happened while we were gone from a unique perspective....my perspective."
Rarity gulped. "Well...what are we waiting for?...As you say...Onwards and upwards..."
"Indeed....Twilight would you do the honors? As much as I'd like to I'm not greatly used to hooves just yet and turning pages is beyond me."
Twilight eyed the tome for a few moments, before taking a deep breath. "Okay." She cast a glance at the sleeping Pinkie Pie... "Let's find out just what's going on here."
She began to read.

Good Evening Dear Diary,

My name is apparently Tick-Tock, I have no prior memories before this date, so I have decided to start chronicling my thoughts to prevent any further loss.
I currently find myself in a small town by the name of Ponyville. I am under the care of a mare by the name of Twilight Sparkle, by whom I was found a few days ago in the Everfree forest. She nursed me back to health and I have only recently awoken. I am very thankful for her hospitality, though at times she seems quite brash. There is something there, in those eyes of hers that I find quite unsettling. But it is not for me to say, she has provided me with room and board until my memory can be regained, I have no place for criticism next to such a generous offer.
She says I am a scientist, and I believe this to be true, I have a profound interest in the way things work. Even now I find myself wondering about the workings of this town, though I have no personal knowledge of my past my mind is filled with calculations and ideas that I itch to bring forth into the world. Hopefully when I am well I will be able to.

----------------

"Skip ahead a few entries," said The Doctor, whatever happened it had to have been in recent years."
Twilight flipped through a few pages.

----------------

Once again I must confide in you dear diary,

I have been under Twilight's care for several months now, but as of late I have hardly seen her. She has locked herself away in the basement of this great library, and is hard at work on something.  She has asked my help several times, but has never let me see the device she is attempting to build. I have asked her companion, a small dragon by the name of Spike, but he knows little more than I. We find ourselves in each other's company more often than not. He is a pleasant if at times childish fellow. From what I gather he and Twilight were quite close at some point. I must wonder if perhaps there was some kind of fallout, as Twilight hardly says a word to either of us in the rare times when she comes out of the basement. Despite this he still seems loyal to the last. The eyes, as I have noted in many entries, have gotten even darker than my last. I worry there is something wrong with the poor girl, but she will not let me examine her. I am beginning to fear for her, though I am as of yet not sure if my worries are warranted.

----------------

Twilight flipped through the next few entries.
----------------

Diary I must cite an odd happening this evening,

There was a knock at the door as I was reading a tome of Equestria history. I have never answered the door, as Twilight has requested I not do so. While I find this an odd request she has been kind to me in her own, distant way, and it would not be right of me if I did not try to adhere to any rules put forth.
I tried my best to ignore this intrusion and continue my studies, but oh diary this visitor was persistent, for hours they hammered at the door until I could not take the noise any longer. I had been living here for nearly a year now, had I not? I thought myself entitled to a little peace, and what harm could it do?
So, emboldened by my annoyance, I opened the door to find a pink pony standing there. I had spied her from afar several times, normally from a window, or among those who visited Twilight every now and again. I opened my mouth to try and tell her that Twilight was busy, but suddenly found myself enfolded in one of the most constricting hugs I have ever endured!
The strange visitor began talking so fast I could hardly comprehend what she was saying. You've never heard such madness! Stories of stone angles, alternate dimensions and doctors, I do fear she is quite mad.
But this is not the strangest thing, dear diary. The strangest is...I find her madness contagious! For no reason I can describe I found myself incomparably happy to see her. As though we were old friends seeing each other anew. Does it have something to do with my lost memories? Even her ramblings seemed oddly familiar. Of course they are utter nonsense, but nonetheless I feel a connection, such a profound feeling that they are somehow important.
But alas, dear diary, before I was able to question her further Twilight came storming out of the darkness of her basement. You've never heard such screaming!
She was furious that I had dared to answer the door, or that this pink visitor should try to talk to me. As she was yelled at the poor girl she looked as though she'd been psychically struck.
Twilight slammed the door in a rage, and shooed me back up into my room, where I have remained for the last day or so. The door has been locked, I am afraid I have angered her quite thoroughly this time. It appears the door rule is to be obeyed at all costs.

----------------

Dear Diary,

It has been mere hours since my last entry, I find that I cannot sleep as nightmares plague my rest. I see such strange things! Stone Pegasus and animate dolls, aliens of all shapes and sizes! Mechanical dogs and bipedal creatures I cannot describe. But I feel as though I know them, that I know this world of dreams. Oh, curse my lack of memory! If only I could fathom there meaning, but alas I cannot.
----------------

The next few pages were filled with sketches, Twilight flipped through them slowly. Some she recognized, and others she did not. One of them appeared to be a Darlock, only without the horse shaped upper portion. It had been circled several times in red.
"Keep reading!" said Rarity.
Twilight quickly flipped through the drawings, and continued. The next few entries recalled fantastic accounts of dreams, and their significance, but nothing of particular interest. She continued through the journal until she found something.

----------------

Dear Diary,

I must apologize for my lack of entries the past few days. I have been busy. Twilight has been asking me more questions than usual, and generally requiring more of me on a day to day basis. I must wonder if it is because she really requires my assistance. Or is simply trying to keep me busy, if Spike is  correct, then I have been talking in my sleep. This apparently has her worried, is she trying to fill my mind by supplying me with other tasks so my dreams will turn to other subjects?
I cannot help but wonder.

----------------

The page following the entry were filled with more Sketches, this time of a small wooden box with
glass in the front.
"The HORN," said the Doctor. "Keep reading, we're coming close to the big event that brought on your rule."

------------------
Diary, something wonderful has happened,

I cannot remember my last entry, for I have been so very busy. You see, dear diary, Twilight has given me access to what she has been working on for all this time.
I have made several sketches, I am not sure of all of it's workings, for sadly I am not a unicorn. But diary that's the thing! Soon I will not have to be! The mechanics are complex, which is why she required my help, but I believe that with this device magic will no longer be reserved for those special few born with the talent! We have worked through the night and she plans to unleash this gift upon the world in mere hours. The excitement is palpable.

------------------

Dear Diary,

I apologize for being haphazard with my updates. It's marvelous, there are several of the devices currently in operation around ponyville. While I myself have not had the honor, it is a wonder to see them in action. HORNs they are called, and such fantastic things they are. Magic for earthponies? A mere dream for many a  young foal, now realized! I can hardly believe it. It seems my fears of Twilight were unfounded. She is an inventor after my own heart, and she has changed the world for the better. She has taken the invention to Cantolot, where I have heard there is trouble. Hopefully it shall be able to help. The princesses, from what I've studied, have been ill for some time. Twilight has taken to helping, making decisions by way of letter. Who knows, with this invention perhaps they can be cured? With this device anything is possible. It will be a golden age for Equestria! And I had a hand in it, though I can remember nothing of my past, I have bright hopes for the future.

----------------
Dear Diary,

I write this in fear, Twilight has returned, and she has changed. Her eyes have taken on the darkest color I have seen on any living creature. This evening I heard her talking to herself in the dark of the basement. I dared not intrude on whatever dark things she's working on. Spike seems just as worried, he has grown, almost too big for the library at this point. I am worried for him as well as Twilight, he is tired as of late. It seems he has some part in the production of the HORNs, but he will not reveal to me what it is. For the last several days he has been more private than usual. When pressed he simply replies 'It's what's best for Twilight.' It is unsettling. I do not know what will happen next, but I feel in my heart that it shall not be good.
---------------

Twilight stopped reading suddenly. The Doctor a hoof on her shoulder.
"I...I think I can deal with the hooves...Would you like me to read the rest?" he asked softly.
Twilight nodded.
The Doctor grabbed the book from it's place in the air, and placed it open on the table
next to the unconscious Pinkie Pie.
"Just remember. None of this is you, time is in flux, never more so than now."
He continued to read.

-------------
Dear Diary,

My worst fears have been realized. Twilight departed for the lantern castle in the Everfree Forest several hours ago, and even from here I can feel the shaking. Something dreadful is happening as I write this account. The entire town has been up all night looking, looking towards the flashes above the trees. It is now nine in the morning, and the sun has not yet risen, it lies on the cusp of the horizon, daring to go no farther. I know I cannot be sure Twilight's hoof is in this, but it is as if I can feel that she is. That something is now wrong with the world, wrong with time itself. I feel compelled to go forth, to do something to stop it. But do not know how I can help. So I remain here, a coward. We can only wait until the noise ends, and hope for the best.

-----------

Things are grave indeed,

She's queen now. Twilight has installed herself as the monarch of Equestria, she's changed, I know not what happened to the princesses, but Twilight now shares their form. She is an alicorn, normally a creature of dreams, turned to a nightmare.
The sun still has not risen, as I stand here, several days from my last entry. It is twilight, it seems, for eternity.
I am packing what little I have. I received a letter stating I have been summoned to Cantorlot, where I am to live, Spike has already gone ahead. Who are we to disobey the queen?
We are no one.

--------------

I have arrived Dear Diary,

The opulence of Cantorlot is lost on me. I have never been far outside of the Library in Ponyville, Twilight never allowed me the pleasure, but in this darkness is there any point?
Alas, I must apologize for being so morose, dear diary, but things are in quite a state. Twilight rules with an iron hoof. It has been mere days since her take over, and already she has launched armies against the Griffin Kingdoms and the mines of the Dimond Dogs. I fear she has been corrupted beyond any help.
Sadly, my stay is not to be long here. Already I have been ordered onto a train that leaves in a few hours. To the Lantern Castle in the Everfree, what she plans for me there I have no idea.
-------------

The Doctor flipped the middle of the diary, many of it's pages singed beyond comprehension, he frowned, and continued to nose through until he got to something legible.

------------

Curses, another failure, and it seems I have burned a large chunk of my records in the explosion. Years of writings, gone. Never to be replaced! Well, I have never been one to dwell on that which cannot be changed. According to what pages remain my last surviving entry is from before I arrived. To reiterate any lost knowledge, I have been here for the past...how long has it been? It is hard to keep track in this dark laboratory.The dark that makes you feel you're not alone.
Day and night are meaningless in anycase. To continue, I have continued work on Twilight's newest tool of war. They have been shipping out for months, and I am beginning to scare myself, but I have no choice but to continue. If I do not she has not only threatened to hurt me, but my only companion. A nurse by the name of Fluttershy, she is charged with the care of the Princesses, who have been in an awful state since Twilight came to power. She brings me food every now and again, and is a kind soul. I could not bear to see her hurt. But I must wonder dear diary, if I have been making the right choice all these years? I feel such loathing for my creation, the Darlocks. I look upon them now, their lone eyes staring back at me, a small bit of life in each.
I have at least done some good in that respect. I do not know how, but I knew what to do the second I began work on them so long ago, and what Twilight wanted me to do. To use ponies, to power these cruel machines....I could not bring myself to do so. So I have delved into deep science. Things which are new, and scary to me. I have grown them, from mere samples of myself. Bits of hair and skin. They are my children....which makes me loathe them even more. Alas, the alternative is unfeasible.
Still I am bothered, it seems my cells are not normal. they grow many times faster than that of any other creature I have encountered when cultivated, and are devilishly hard to kill. I have begun to wonder.
What am I?
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Dear Diary

I have received new plans, plans for a machine under the capitol. It's awful.
I know why I don't feel alone in the dark. I know what she's planning. Yet I have no choice.
Once again I find myself a coward. I dare not write further on the subject.

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Dear Diary,

I have begun to understand the darkness better. Through study I have found that it is not one mass, but several smaller, almost microbial life forms feeding in the air. They make up the blackness around me. That is why my laboratory must stay in the dark. They are part of the Darlocks, but not only that, they are my guards, and her insurance, they could devour me in seconds. Or Fluttershy for that matter, should they get the inclination. I now know why the princesses were raving, why they constructed the castle above me, filled with lights to banish the shadows. I know why they are afraid of the dark. If only they knew what lay below them, it would scare them to death.
Yet I am unharmed. I must wonder how she controls them. If I can figure that out, I will no longer be in danger, perhaps then we can escape.
But where would we go? She cannot leave the princesses unattended and they are hardly in any shape to travel. Twilight would find us in a matter of days if not hours. It seems a hopeless task.

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Dear Diary,

Suddenly I feel as though Fluttershy and I are not alone in this castle. I have grown used to the Darkness's intrusion, but it feels as though there is something new. I am cautious, it may be some new agent of Twilight's power, sent to keep an eye on me. I am wary.

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Dear Diary,

Let me start from the beginning for the first time in many years I feel hopeful. My fears of a new threat have proven wrong, in fact we have a new ally. One that is desperately needed.
It happened yesterday. I had come out of the lab in order to have lunch, Fluttershy had scraped together something extra from the Princess's meager stores in order to spice up the usual hay and oats. She does what she can to make our lives a touch brighter. It made me feel a touch poorly for taking lunch alone. My years of solitude seem to have left their mark.
In anycase, I was eating as usual when suddenly right behind me I heard laughter....Such a curious thing, not only for it's abruptness, but because it had been so long since I'd heard any. I was badly frightened by this, spilling my lunch all over the floor.
But when I turned to find the source of the sound I saw her.
The pink pony from all those years ago. The one at the door who spoke of nonsense, she was standing right there, as smile on her face bigger than any I'd ever seen.
My fear was replaced by sheer amazement. How had she found me? Or gotten here? She wore the official clothes of the royal planner. I thought for a moment that perhaps she was here to deliver a message, or some news from the capital. Before I was able to voice any of my many questions I found myself once again in a hug which forced all the air from my lungs, apparently her customary greeting. She, Pinkie Pie, called me 'Doctor' and rattled on so fast I couldn't understand a word after that.
Once she calmed down she informed me that she has run away from Twilight's castle in Cantorlot, where she has been employed for the last couple years. Apparently because Twilight has 'Become a meany.' which is the single biggest understatement I shall ever write.
She apparently found me by way of 'Pinkie Sense' whatever the term may mean. She said she had the feeling that something big was about to fall, and pointed to her ever moving tail as a reference. I still understand little of this, but I am glad to have another friendly face. Her happiness is ever contagious, I find myself smiling as she dances about the room, talking faster than I can comprehend.
She says we must keep her presence a secret from Fluttershy. Ponies will come looking for her, and Fluttershy is far too sweet to lie, or at least lie well. So her ignorance is best for the time being. She offered to hide in my lab which I was vehemently against, knowing what darkness lies there.
Still she marched on, unafraid, to the edge of the stairs, where the light ended. She knew what was down there, and simply reasoned with it.
I don't know how, or why this worked, but she said that there was only supposed to be one pony down there, so therefor if she was going down there with me willingly knowing what might happen, then she must not be a pony.
Then she stepped downwards. Into the dark.
And was fine.
I've often wondered, since discovering my cells seem abnormal, what I am. Now I find myself wondering....What is she?

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Dear Diary,

It seems Pinkie was right, Twilight has begun a massive search for her. A pair of those awful living dolls she employs searched the castle today. Fluttershy says she's never seen the princesses so scared. Still, as Pinkie predicted, they did not look inside the lab, and left having found no trace of her. It seems she is safe for the time being.

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Dear Diary

I have told Pinkie of Twilight's plans for what lies beneath the castle, and of my hand in it. She was just as dismayed as I to learn of this. We have begun to plan against it. We have nothing yet, but we must stop her terrible ambitions, lest everything we know, and in fact what we do not, be threatened.
While we worked she continued to tell her stories, the same ones from when we first met. Apparently this 'Doctor', whom she believes to be me, is some kind of hero. I am far from this. I have told her of this mistake, I am but a scientist, but still she persists. Saying I knew her, and Twilight before waking up with nothing all those years ago, saved Equestria. I wish this were true, it would explain the ever present gap in my memory. But it is simply absurd.
All they are is stories...

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Dear Diary

It has happened. She is here, to check on my progress, queen Twilight has come here, and she is even  less the mare I once knew than ever. I have shown her the Darlocks, almost ready for her evil plans, while Pinkie hides among the Princesses. Fluttershy is still nonethewiser. This is perhaps for the best, Pinkie Pie was correct, the poor sweet hearted mare was almost in tears from the simplest of questions on the princesses' status. Feeling guilty for giving me what food she could. I cannot imagine burdening her with such a secret.
But, hiding Pinkie Pie shall not be easy, Twilight appears to be staying for the next few days to monitor my work. I fear that she knows more than she is letting on.

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Dear Diary
I am not sure whether I should be happy, or sick to my stomach. Twilight is very pleased with my efforts towards creating her war machines. She plans to leave tomorrow night to begin preparations. I dearly fear what may happen, but at least we shall be rid of her, and we'll have the time we need.
Time.
What a funny concept these days. After all these years, I, nor Fluttershy nor Pinkie has aged a single day....I believe the HORNs have something to do with it...but...I've never had a Horn. So I must wonder...what is my excuse?  My theory must be flawed. In anycase, Pinkie and I have come up with a plan to stop her, a device which, when planted into the machine under the capital will disable it, and perhaps allow me time to make sure it never sees its terrible work done...for you see Twilight has ruined one world...I shall not let her ruin another.

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All that planning....to waste...She found us....She came...into the laboratory the night she was set to leave, totally unannounced....Pinkie Pie was hidden among the monstrosities, but I think we both knew something was off. She seemed a bit too happy....Twilight circled the lab like a shark, taking glee in my fear. She said she'd never seen the Darlock's newest weapon in action, and that it would be nice to test it. She was cruel in her teasing...she offered to go and grab Fluttershy for a test run, and that was all Pinkie could take. She leapt out of the darkness with and offered herself to Twilight in the poor nurse's place. I leapt to protect her, but found myself wrapped in the bonds of Twilight's ethereal tail, forced to watch as she was punished for betraying the queen.
The funny thing is...Pinkie seemed happy to see Twilight, for all she had done...the poor girl smiled and laughed, even joking as the queen activated one of the monsters. And for a moment... just for a moment, Twilight's eyes lightened, and she looked sad. Genuinely and properly sad. But, like anything in this horrid lab, it was quickly extinguished as the newly awakened darlock fired, striking Pinkie squarely in the chest. Her laughter stopped, and her color faded.
You see, the darlocks are not a forceful weapon...no...the darkness that permeates my workspace is part of them....and that darkness...that horrible...oppressive darkness can do more than devour...it can change. Smother the synapses and darken the mind as well as the air. Taking joy and happiness and leaving mindless drones...this is what she plans for Equestria....and worlds beyond...darkness, inside and out...eternal twilight of the body and mind. A ever feeding, ever growing stain upon the universe.
And I let it happen.
I sat there as Pinkie's happiness was drained away in an instant.
Or at least as the darkness tried to.
You see, I think that some people are just happy...naturally...properly happy. They're few and far inbetween...but if anyone is...it's Pinkie. There is a light inside her so bright that it could outshine the hidden sun. And no amount of science or magic, could ever truly change that.
She fought, dear diary. Her mane and tail went straight as silk, but still, she smiled a bit at Twilight, and said she'd see her soon, in happier times. She danced about the lab like a filly, occasionally grimacing or struggling, but doing so nonetheless. Twilight was put momentarily enraged....but for some reason...she did not strike out against the pink pony...I think that light inside stopped her...that bit of good still fighting among the darkness as Pinkie did then. She simply left. Leaving Pinkie barely standing among the darlocks. She released me and vanished into the night to put her horrible plans into action.
I had little time to act....I gave Pinkie a sedative of my own creation, I have applied a dose every few hours. It slows the process going on in her head....but I wonder to what end? Hers is perhaps the fate that awaits us all....still I must...I must have hope. There is a light in her, and I think that perhaps that light, a light that is in every being that has ever known joy, may be the only thing that can stop the darkness. If I am wrong, then all is lost. I dearly hope some poor soul should figure this out, as I am too afraid to act further. If I do, I fear what may happen to Fluttershy and the princesses. I continue my work in my prison...alone.

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The journal entries ended, the Doctor closed the book with a sharp thud. He stared hard at the small journal for several moments, then down the stairwell. Twilight sat on her haunches, exhausted by all the information she'd taken in.
Rarity made a quite sound. "They're...made from you....and Pinkie....Twilight she..."
The Doctor simply nodded his expression never changing.
Twilight took a deep breath. She looked back at Tick-Tock who's breathing had grown more fitful as they'd read.
"I....did that...to you?"
The Doctor's head whipped around to look at her, she didn't flinch. He stared at her for several seconds, his deep blue eyes burning with something deep and old.
He was the first one to break away. "No..." The Doctor looked at the ground. "I was the one that did this to you..."
Twilight paused. "Doctor...what do you mean?...Did what?"
The timelord sighed. "You've known things...since the toyshop haven't you? I've pointed it out before now, kept saying I'd explain later...But...perhaps I was hoping it wasn't true."
Rarity stared at the Doctor worriedly. "What...wasn't true?"
"Back in our present, to stop the reaper I let you look into my head...but I underestimated you...and gave a lot more than I intended...You may have already guessed that much."
Twilight nodded. "I've...been thinking about it since I knew how to fix the TARDIS...back before we came here."
"Well, that alone was not enough to make you do all of this. Back then, way back, when we were looking for her." He pointed to Fluttershy, who made a soft surprised noise. "She said her bunnies had gone missing, and I thought that the reason must've been some sort of predator, something that was already in the habitats."
"Yes..." Twilight prompted.
"I didn't have the time to think about it, but what's in every rabbit hole? Every din and every burrow? A shadow." He gestured towards the stairwell, the light stopping after the first step to be swallowed by the dark. "And in the dark, sometimes things go missing...the Vashta Nerada. So, in that chain of events, you, Twilight Sparkle, got a bit of timelord in your head, and I, put it there."
"So lets say this timeline ran a bit differently. Let's say that you and I solve this problem, or its a different one, or we somehow make it back home. Then we go investigate the 'Strange creatures in Fluttershy's little garden.'" The Doctor laughed almost ruefully. "And what do they find when Twilight Sparkle bumbles into the dark? A meal? Oh, oh no, they find something greater than that. You see, me? All that knowledge is safely locked up in my head, they could eat me if they like, it'd take'em a while with the regenerations and all, but they could, and nothing'd happen. But you...oh your mind is wide open. And as they set in...they find a spark of knowledge so great it inspires them...tells them they can do more than eat, more than just mindlessly feed...that they can rule. And oh here's the perfect little vehicle to do it in. Just turn down the light in that mind a little, just a touch here and there, tiny things at first. Then they start to turn up the dark. Slowly and steadily altering you, microscopic spores of darkness in your head." He turned to her, his face sad and lonely. "With all the darkness around us now, they might have started again already....a chain of events going round and round, I take you back, you run into them, they change you...you become ruler of Equestria and set out to spread darkness wherever you can. All because I was too stupid to notice." The Doctor took Twilight's head between his hooves, and planted a small kiss on her forehead. "I'm sorry Twilight Sparkle. Very, very sorry. But this is not your fault. It's mine."
Silence filled the room, heavy and thick for several minutes. The only sounds the soft breaths of the two sleeping ponies on either side of them, each going through their own nightmares.
"How do we stop it." Twilight said finally.
The Doctor didn't say anything.
Twilight repeated herself. "How.Do we. Stop it."
Rarity gave the Doctor a hopeful look, but he remained silent.
"Doctor?" Twilight said.
He managed, to look up, only for a hoof to meet the side of his jaw. He spun a bit before falling to the ground.
"Hey!" He yelled.
"You will not give up on me." Twilight stood over him fuming. "You fall out of the sky into my house, get me kidnapped by evil statues, destroyed several reputable businesses around Ponyville, implant the knowledge of an ancient race into my brain, get me flung into a horrible future where half my friends are under my tyrannical rule, my mentor is half crazed, the sun never rises and there are living dolls roaming the streets, and you think I'm just going to let you sit there like an idiot?"
The Doctor looked up at her, totally stunned.
"If you do then you've got another thing coming. Now get off your flank, get that sonic screwdriver of yours, out of your coat pocket, and help me fix this. Now. I'm tired of being scared of everything, I'm tired of worrying that I'm going to be some horrible pony fifty years down the line. And I'm really sick of my friends being treated this way by someone who will never be me. I don't care what you did, what you've done, or what you're going to do. What you're doing now is fixing this. Are. We. Clear?"
Both the Doctor and Rarity stared at Twilight mouths agape.
"Well," The Doctor was the first to speak. "When you put it that way." He hopped up and headed towards Tick-Tock. "Let's get started. Melvin, pick up Pinkie Pie." The Doctor hefted Tick-Tock onto his back, then flung the unconscious pony in Melvin's general direction, despite Fluttershy's weak protests. "This too, who knows, I might be useful eventually." He headed towards the door out into the castle proper.
"That's more like it." Twilight joined him at his side, a still stunned Rarity bringing up the rear. "Where are we going?"
"We need to have a word with your mentor, and then we need to find transportation. Quickly."
"So we can get back to canterlot and find the TARDIS?"
The Doctor nodded. "That and because if my ears don't fail me, there's a train coming."
Rarity blinked. "There's only one other train that comes this way..."
"Twilighttwo's personal locomotive?" The Doctor guessed.
Rarity looked worriedly towards the nearest window. "Um...yes."
"Figured that, with a full complement of fully functional Darlocks no doubt."
Twilight stared at the two of them for a second, before quickening her pace. "Yeah...Let's hurry."

982 C.R

"Then what happened! Then what happened!" Trixie yelled, jumping up and down as the Doctor spun his tale.
He gave her a little smile and said.
"Then came the hard part."

To be continued.